Kevin Coombes

Publications

Thesis

Research Journals

  1. K. R. Coombes and V. Srinivas. Relative K-theory and vector bundles on certain singular varieties., Invent. Math.. 1982; 70:1--12.
  2. K. R. Coombes. Relative algebraic K-theory., Invent. Math.. 1982; 70:13--25.
  3. K. R. Coombes and V. Srinivas. A remark on K1 of an algebraic surface., Math. Ann.. 1983; 265:335-342.
  4. K. R. Coombes. On SK1 of curves and Kähler differentials., Com. Alg.. 1985; 13:697--716.
  5. K. R. Coombes and D. J. Muder. Zero cycles on del Pezzo surfaces over local fields., J. Alg.. 1985; 97:438--460.
  6. K. R. Coombes and D. Harbater. Hurwitz families and arithmetic Galois groups. Duke Math. J.. 1985; 52:821--839.
  7. K. R. Coombes and R. J. Fisher. Inversion of abelian integrals on curves of small genus. Math. Ann.. 1986; 275:185--196.
  8. K. R. Coombes. Motifs, L-functions, and the K-cohomology of rational surfaces over finite fields. Math. Ann.. 1987; 276:255--267.
  9. K. R. Coombes. On the K-theory of curves over finite fields. J. Pure Appl. Alg.. 1988; 51:79--87.
  10. K. R. Coombes. Every rational surface is separably split. Comm. Math. Helv.. 1988; 63:305--311.
  11. D. McCoy-Pardington, W. J. Judd, P. Knafl, L. V. Abruzzo, K. R. Coombes, S. H. Butch and H. A. Oberman. Blood utilization during extracorporeal membrane oxygenation. Transfusion.. 1990; 30:303--309.
  12. K. R. Coombes and D R. Grant. On heterogeneous spaces. J. Lon. Math. Soc.. 1989; 40:385--397.
  13. K. R. Coombes. The arithmetic of zero cycles on surfaces with geometric genus and irregularity zero. Math. Ann.. 1991; 291:429--452.
  14. K. R. Coombes and M. Potegal. Attack priming and aggressive arousal in female Syrian golden hamsters, Mesocritus auratus: Observed attack latency and calculated attack probability as a function of contact time with a conspecific. Animal Behavior. 1994.
  15. Coombes, K.R. Elliptic curves and logarithmic derivatives. J. Pure Appl. Alg.. 1999; 138:21-38.
  16. Taylor, E., Cogdell, D., Coombes, K.R., Hu, L., Ramdas, L., Tabor, A., Hamilton, S., Zhang, W. Sequence verification as a quality control step in the production of cDNA microarrays. Biotechniques. 2001; 31:62-65.
  17. Hess, K.R., Zhang, W., Baggerly, K.A., Stivers, D.N., Coombes, K.R. Microarrays: handling the deluge of data and extracting reliable information. Trends in Biotech.. 2001; 11:463 - 468.
  18. Zhang, W., Labordé, P.M., Coombes, K.R., Berry, D., Hamilton, S. Cancer genomics: Promises and complexities. Clinical Cancer Research.. 2001; 7:2159-2167.
  19. Baggerly, K.A., Coombes, K.R., Hess, K.R., Stivers, D.N., Abruzzo, L.V., Zhang, W. Identifying differentially expressed genes in cDNA microarray experiments. J Comp Biol.. 2001; 8:639-659.
  20. Ramdas, L., Coombes, K.R., Baggerly, K.A., Abruzzo, L.V., Highsmith, W.E., Krogmann, T., Hamilton, S., Zhang, W. Linearity of cDNA microarray expression measurements: caveats, serial dilutions, and quality controls. Genome Biology.. 2001; 2:research0047.1 - 0047.7.
  21. Coombes, K.R., Highsmith, W.E., Krogmann, T.A., Baggerly, K.A., Stivers, D.N., Abruzzo, L.V. Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. J Comp Biol.. 2002; 9:655-669.
  22. Hu, L., Wang, J., Baggerly, K.A., Wang, H., Fuller, G., Hamilton, S., Zhang, W. Coombes, K.R. Obtaining reliable information from minute amounts of RNA using cDNA microarrays. BMC Genomics.. 2002; 3:16.
  23. Coombes, K.R., Zhang, L., Bueso-Ramos, C., Brisbay, S., von Eschenbach, A., Logothetis, C., Roth, J., McDonnell, T. TAD: a web interface and database for tissue microarrays. Applied Bioinformatics. 2002; 1(3):155-8.
  24. Wang, J., Hu, L., Hamilton, S.R., Coombes, K.R., Zhang, W. RNA amplification strategies for cDNA microarray experiments. Biotechniques.. 2003; 34:394-400.
  25. McCarthy H, Wierda WG, Barron LL, Cromwell CC, Wang J, Coombes KR, Rangel R, Elenitoba-Johnson KS, Keating MJ, Abruzzo LV. High expression of activation-induced cytidine deaminase (AID) and splice variants is a distinctive feature of poor-prognosis chronic lymphocytic leukemia. Blood. 2003; 101:4903-8.
  26. Udtha M, Lee SJ, Alam R, Coombes K, Huff V. Upregulation of c-MYC in WT1-mutant tumors: assessment of WT1 putative transcriptional targets using cDNA microarray expression profiling of genetically defined Wilms' tumors. Oncogene. 2003; 22:3821-6.
  27. Goy A, Ramdas L, Remache YK, Gu J, Fayad L, Hayes KJ, Coombes KR, Barkoh BA, Katz R, Ford R, Cabanillas F, Gilles F. Establishment and characterization by gene expression profiling of a new diffuse large B-cell lymphoma cell line, EJ-1, carrying t(14;18) and t(8;14) translocations. Lab Invest. 2003; 83:913-6.
  28. Baggerly KA, Morris JS, Wang J, Gold D, Xiao LC, Coombes KR. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics. 2003; 3:1667-72.
  29. Coombes KR, Fritsche HA Jr, Clarke C, Chen JN, Baggerly KA, Morris JS, Xiao LC, Hung MC, Kuerer HM. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem. 2003; 49:1615-23.
  30. Morris JS, Baggerly KA, Coombes KR. Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE. Biometrics. 2003; 59:476-86.
  31. Spurgers KB, Coombes KR, Meyn RE, Gold DL, Logothetis CJ, Johnson TJ, McDonnell TJ. A comprehensive assessment of p53-responsive genes following adenoviral-p53 gene transfer in Bcl-2-expressing prostate cancer cells. Oncogene. 2004; 23:1712-23.
  32. Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, Koo JS, Kapoor M. A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays. BMC Genomics Jan; 5:2.
  33. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics. 2004; 20:777-85.
  34. Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics. 2004; 20:3166-78.
  35. Kuerer HM, Coombes KR, Chen JN, Xiao L, Clarke C, Fritsche H, Krishnamurthy S, Marcy S, Hung MC, Hunt KK. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery. 2004; 136:1061-9.
  36. Baggerly KA, Edmonson SR, Morris JS, Coombes KR. High-resolution serum proteomic patterns for ovarian cancer detection. Endocr Relat Cancer. 2004; 11:583-4.
  37. Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics. 2005; 21:1764-75.
  38. Pawlik TM, Fritsche H, Coombes KR, Xiao L, Krishnamurthy S, Hunt KK, Pusztai L, Chen JN, Clarke CH, Arun B, Hung MC, Kuerer HM. Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry. Breast Cancer Res TreatKoomen JM, Shih LN, Coombes KR, Li D, Xiao LC, Fidler IJ, Abbruzzese JL, Kobayashi R. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res. 2005; 11:1110-8.
  39. Ji Y, Wu C, Liu P, Wang J, Coombes KR. Applications of beta-mixture models in bioinformatics. Bioinformatics. 2005; 21:2118-22.
  40. Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst. 2005; 97:307-9.
  41. Hu J, Coombes KR, Morris JS, Baggerly KA. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic. 2005; 3:322-31.
  42. Esteva FJ, Sahin AA, Cristofanilli M, Coombes K, Lee SJ, Baker J, Cronin M, Walker M, Watson D, Shak S, Hortobagyi GN. Prognostic role of a multigene reverse transcriptase-PCR assay in patients with node-negative breast cancer not receiving adjuvant systemic therapy. Clin Cancer Res. 2005; 11:3315-9.
  43. Abruzzo LV, Lee KY, Fuller A, Silverman A, Keating MJ, Medeiros LJ, Coombes KR. Validation of oligonucleotide microarray data using microfluidic low-density arrays: a new statistical method to normalize real-time RT-PCR data. Biotechniques. 2005; 38:785-92.
  44. Koomen JM, Li D, Xiao LC, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res. 2005; 4:972-81.
  45. Abruzzo LV, Wang J, Kapoor M, Medeiros LJ, Keating MJ, Highsmith WE, Barron LL, Cromwell CC, Coombes KR. Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays. J Mol Diagn. 2005; 7:337-45.
  46. Stec J, Wang J, Coombes K, Ayers M, Hoersch S, Gold DL, Ross JS, Hess KR, Tirrell S, Linette G, Hortobagyi GN, Symmans WF, Pusztai L. Comparison of the Predictive Accuracy of DNA Array-Based Multigene Classifiers across cDNA Arrays and Affymetrix GeneChips. J Mol Diagn. 2005; 7:357-67.
  47. Coombes, K.R., Koomen, J.M., Baggerly, K.A., Morris, J.S., Kobayashi, R. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Informatics. 2005; 1:41-52.
  48. Baggerly, K.A., Coombes, K.R., Morris, J.S. Bias, randomization, and ovarian proteomic data: A reply to "Producers and Consumers". Cancer Informatics. 2005; 1:9-14.
  49. Coombes, K.R., Tsavachidis, S., Morris, J.S., Baggerly, K.A., Hung, M.C., Kuerer, H.M. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics. To appear.
  50. Gold, D.L., Wang, J., Coombes, K.R. Inter-gene correlation on oligonucleotide arrays: how much does normalization matter? PharmacoGenomics. To appear.
  51. Hu, J., Kapoor, M., Zhang, W., Hamilton, S.R., Coombes, K.R. Analysis of dose-response effects on gene expression data with comparison of two microarray platforms. Bioinformatics. To appear.
  52. Yokoi, K., Shih, L.N., Kobayashi, R., Koomen, J., Hawke, D., Li, D., Hamilton, S.R., Abbruzzese, J.L., Coombes, K.R., Fidler, I.J. Serum amyloid A as a tumor marker in sera of nude mice with orthotopic pancreatic cancer and in plasma of patients with pancreatic cancer. . To appear.

Editorials

  1. Coombes KR. Analysis of mass spectrometry profiles of the serum proteome. Clin Chem. 2005; 51:1-2.
  2. Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics profiling--a young technology begins to mature. Nat Biotechnol. 2005; 23:291-2.
  3. Lahad JP, Mills GB, Coombes KR. Stem cell-ness: a "magic marker" for cancer. J Clin Invest. 2005; 115:1463-7.

Referred Conference Proceedings

  1. K. R. Coombes. Local class field theory for curves In Applications of Algebraic K-theory to Algebraic Geometry and Number Theory, Part I, volume 55 of Contemporary Math, pages 117--134. AMS, 1986.
  2. K. R. Coombes. The arithmetic of Enriques surfaces In Proceedings of a Conference on K-theory, Commutative Algebra, and Algebraic Geometry, Santa Margherita, volume~126 of Contemporary Math., pages 47--57. AMS, 1992.
  3. Baggerly, K.A., Coombes, K.R., Hess, K.R., Stivers, D.N., Abruzzo, L.V., Zhang, W. Studentizing microarray data. In: Computational and Statistical Approaches to Genomics, Kluwer Academic Press, Norwell MA, 2002, pages 53-64.
  4. Wang, J., Coombes, K.R., Baggerly, K.A., Hu, L., Hamilton, S.R., Zhang, W. Statistical considerations in the assessment of cDNA microarray data obtained using amplification. In: Computational and Statistical Approaches to Genomics, Kluwer Academic Press, Norwell MA, 2002, pages 23-39
  5. Coombes, KR, Baggerly, KA, Stivers, DN, Wang, J, Gold, D, Sung, HG, Lee, SJ. Biology-Driven Clustering of Microarray Data: Applications to the NCI60 Data Set. In: Methods of Microarray Data Analysis II, Kluwer Academic Publishers, Boston, 2002, pages 65-79.
  6. Stivers, D.N., Wang, J., Rosner, G.L., Coombes, K.R. Organ-specific differences in gene expression and UniGene annotations describing source material. In: Methods of Microarray Data Analysis III, Kluwer Academic Publishers, Boston, 2003, pages 59-72.
  7. Coombes, K.R., Wang, J., Abruzzo, L.V. Monitoring the quality of microarray experiments. In: Methods of Microarray Data Analysis III, Kluwer Academic Publishers, Boston, 2003, pages 25-40.
  8. Zhang, L., Coombes, K.R., Xiao, L.C. Quantification of cross hybridization on oligonucleotide microarrays. In: Methods of Microarray Data Analysis III, Kluwer Academic Publishers, Boston, 2003, pages 175-184.

Books

  1. K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck. Differential Equations with Mathematica. John Wiley and Sons, New York, 1995.
  2. K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck. Differential Equations with Mathematica, Second Edition. John Wiley and Sons, New York, 1998.
  3. K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck. Differential Equations with Maple. John Wiley and Sons, New York, 1996.
  4. K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck. Differential Equations with Maple, Second Edition. John Wiley and Sons, New York, 1997.
  5. K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck. The Mathematica Primer. Cambridge University Press, Cambridge, 1998.
  6. Coombes, K.R., Lipsman, R, and Rosenberg, J. Multivariable Calculus and Mathematica, with Applications to Geometry and Physics. TELOS, an imprint of Springer-Verlag, New YORK, 1998.
  7. K. R. Coombes, B. R. Hunt, R. L. Lipsman, J. E. Osborn, and G. J. Stuck. Differential Equations with MATLAB. John Wiley and Sons, New York, 1999.

Computer Programs

  1. K. R. Coombes and D. R. Grant. Arithmetic in global fields: A library of C functions. Freely distributed under terms of the GNU Public License.

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